If you extend this class in a decode pipeline component (for example), you can override the TranslateDocType method and strip the DOCTYPE declaration from the incoming message; its a bit fiddly, but it is possible.
If you want a more low-tech approach, load the Xml Message into a string and remove the DOCTYPE using a find/replace pattern, or stick it through some XSLT that maps back to itself but without the DOCTYPE. Both of these approaches are easily doable, but you will incur a large performance hit with large messages.